SMTL ID : 9cyd.1

SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x 01: (1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol

01.1: 18 residues within 4Å: Chain A: L.165, G.166, D.167, V.168, R.169, E.170, M.211, G.212, S.248, A.249, P.250, P.251, Y.267, G.269, N.270, Y.271, Y.276, T.304 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.167, A:P.250, A:P.251, A:Y.267 Hydrogen bonds: A:Y.271, A:Y.271 Salt bridges: A:D.167 pi-Cation interactions: A:Y.267

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.192, T.194, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229 ZN.3: 1 residues within 4Å: Chain A: C.273 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.273

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: G.269, N.270, C.273 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

M Bader, S. et al., A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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